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vigra/seededregiongrowing3d.hxx
00001 /************************************************************************/
00002 /*                                                                      */
00003 /*     Copyright 2003-2007 by Kasim Terzic, Christian-Dennis Rahn       */
00004 /*                        and Ullrich Koethe                            */
00005 /*                                                                      */
00006 /*    This file is part of the VIGRA computer vision library.           */
00007 /*    The VIGRA Website is                                              */
00008 /*        http://hci.iwr.uni-heidelberg.de/vigra/                       */
00009 /*    Please direct questions, bug reports, and contributions to        */
00010 /*        ullrich.koethe@iwr.uni-heidelberg.de    or                    */
00011 /*        vigra@informatik.uni-hamburg.de                               */
00012 /*                                                                      */
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00020 /*    conditions:                                                       */
00021 /*                                                                      */
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00024 /*    Software.                                                         */
00025 /*                                                                      */
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00028 /*    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND          */
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00033 /*    OTHER DEALINGS IN THE SOFTWARE.                                   */
00034 /*                                                                      */
00035 /************************************************************************/
00036 
00037 #ifndef VIGRA_SEEDEDREGIONGROWING_3D_HXX
00038 #define VIGRA_SEEDEDREGIONGROWING_3D_HXX
00039 
00040 #include <vector>
00041 #include <stack>
00042 #include <queue>
00043 #include "utilities.hxx"
00044 #include "stdimage.hxx"
00045 #include "stdimagefunctions.hxx"
00046 #include "seededregiongrowing.hxx"
00047 #include "multi_pointoperators.hxx"
00048 #include "voxelneighborhood.hxx"
00049 
00050 namespace vigra {
00051 
00052 namespace detail {
00053 
00054 template <class COST, class Diff_type>
00055 class SeedRgVoxel
00056 {
00057 public:
00058     Diff_type location_, nearest_;
00059     COST cost_;
00060     int count_;
00061     int label_;
00062     int dist_;
00063 
00064     SeedRgVoxel()
00065     //: location_(0,0,0), nearest_(0,0,0), cost_(0), count_(0), label_(0)
00066     {
00067         location_ = Diff_type(0,0,0);
00068         nearest_ = Diff_type(0,0,0);
00069         cost_ = 0;
00070         count_ = 0;
00071         label_ = 0;
00072     }
00073 
00074     SeedRgVoxel(Diff_type const & location, Diff_type const & nearest,
00075                 COST const & cost, int const & count, int const & label)
00076     : location_(location), nearest_(nearest),
00077       cost_(cost), count_(count), label_(label)
00078     {
00079         int dx = location_[0] - nearest_[0];
00080         int dy = location_[1] - nearest_[1];
00081         int dz = location_[2] - nearest_[2];
00082         dist_ = dx * dx + dy * dy + dz * dz;
00083     }
00084 
00085     void set(Diff_type const & location, Diff_type const & nearest,
00086              COST const & cost, int const & count, int const & label)
00087     {
00088         location_ = location;
00089         nearest_ = nearest;
00090         cost_ = cost;
00091         count_ = count;
00092         label_ = label;
00093 
00094         int dx = location_[0] - nearest_[0];
00095         int dy = location_[1] - nearest_[1];
00096         int dz = location_[2] - nearest_[2];
00097         dist_ = dx * dx + dy * dy + dz * dz;
00098     }
00099 
00100     struct Compare
00101     {
00102         // must implement > since priority_queue looks for largest element
00103         bool operator()(SeedRgVoxel const & l,
00104                         SeedRgVoxel const & r) const
00105         {
00106             if(r.cost_ == l.cost_)
00107             {
00108                 if(r.dist_ == l.dist_) return r.count_ < l.count_;
00109 
00110                 return r.dist_ < l.dist_;
00111             }
00112 
00113             return r.cost_ < l.cost_;
00114         }
00115         bool operator()(SeedRgVoxel const * l,
00116                         SeedRgVoxel const * r) const
00117         {
00118             if(r->cost_ == l->cost_)
00119             {
00120                 if(r->dist_ == l->dist_) return r->count_ < l->count_;
00121 
00122                 return r->dist_ < l->dist_;
00123             }
00124 
00125             return r->cost_ < l->cost_;
00126         }
00127     };
00128 
00129     struct Allocator
00130     {
00131         ~Allocator()
00132         {
00133             while(!freelist_.empty())
00134             {
00135                 delete freelist_.top();
00136                 freelist_.pop();
00137             }
00138         }
00139 
00140         SeedRgVoxel * create(Diff_type const & location, Diff_type const & nearest,
00141                              COST const & cost, int const & count, int const & label)
00142         {
00143             if(!freelist_.empty())
00144             {
00145                 SeedRgVoxel * res = freelist_.top();
00146                 freelist_.pop();
00147                 res->set(location, nearest, cost, count, label);
00148                 return res;
00149             }
00150 
00151             return new SeedRgVoxel(location, nearest, cost, count, label);
00152         }
00153 
00154         void dismiss(SeedRgVoxel * p)
00155         {
00156             freelist_.push(p);
00157         }
00158 
00159         std::stack<SeedRgVoxel<COST,Diff_type> *> freelist_;
00160     };
00161 };
00162 
00163 } // namespace detail
00164 
00165 /** \addtogroup SeededRegionGrowing
00166     Region segmentation and voronoi tesselation
00167 */
00168 //@{
00169 
00170 /********************************************************/
00171 /*                                                      */
00172 /*                    seededRegionGrowing3D             */
00173 /*                                                      */
00174 /********************************************************/
00175 
00176 /** \brief Three-dimensional Region Segmentation by means of Seeded Region Growing.
00177 
00178     This algorithm implements seeded region growing as described in
00179 
00180     The seed image is a partly segmented multi-dimensional array which contains uniquely
00181     labeled regions (the seeds) and unlabeled voxels (the candidates, label 0).
00182     Seed regions can be as large as you wish and as small as one voxel. If
00183     there are no candidates, the algorithm will simply copy the seed array
00184     into the output array. Otherwise it will aggregate the candidates into
00185     the existing regions so that a cost function is minimized.
00186     Candidates are taken from the neighborhood of the already assigned pixels, 
00187     where the type of neighborhood is determined by parameter <tt>neighborhood</tt>
00188     which can take the values <tt>NeighborCode3DSix()</tt> (the default) 
00189     or <tt>NeighborCode3DTwentySix()</tt>. The algorithm basically works as follows 
00190     (illustrated for 6-neighborhood, but 26-neighborhood works in the same way):
00191 
00192     <ol>
00193 
00194     <li> Find all candidate pixels that are 6-adjacent to a seed region.
00195     Calculate the cost for aggregating each candidate into its adajacent region
00196     and put the candidates into a priority queue.
00197 
00198     <li> While( priority queue is not empty)
00199 
00200         <ol>
00201 
00202         <li> Take the candidate with least cost from the queue. If it has not
00203         already been merged, merge it with it's adjacent region.
00204 
00205         <li> Put all candidates that are 4-adjacent to the pixel just processed
00206         into the priority queue.
00207 
00208         </ol>
00209 
00210     </ol>
00211 
00212     <tt>SRGType</tt> can take the following values:
00213     
00214     <DL>
00215     <DT><tt>CompleteGrow</tt> <DD> produce a complete tesselation of the volume (default).
00216     <DT><tt>KeepContours</tt> <DD> keep a 1-voxel wide unlabeled contour between all regions.
00217     <DT><tt>StopAtThreshold</tt> <DD> stop when the boundary indicator values exceed the 
00218                              threshold given by parameter <tt>max_cost</tt>.
00219     <DT><tt>KeepContours | StopAtThreshold</tt> <DD> keep 1-voxel wide contour and stop at given <tt>max_cost</tt>.
00220     </DL>
00221 
00222     The cost is determined jointly by the source array and the
00223     region statistics functor. The source array contains feature values for each
00224     pixel which will be used by the region statistics functor to calculate and
00225     update statistics for each region and to calculate the cost for each
00226     candidate. The <TT>RegionStatisticsArray</TT> must be compatible to the
00227     \ref ArrayOfRegionStatistics functor and contains an <em> array</em> of
00228     statistics objects for each region. The indices must correspond to the
00229     labels of the seed regions. The statistics for the initial regions must have
00230     been calculated prior to calling <TT>seededRegionGrowing3D()</TT>
00231 
00232     For each candidate
00233     <TT>x</TT> that is adjacent to region <TT>i</TT>, the algorithm will call
00234     <TT>stats[i].cost(as(x))</TT> to get the cost (where <TT>x</TT> is a <TT>SrcImageIterator</TT>
00235     and <TT>as</TT> is
00236     the SrcAccessor). When a candidate has been merged with a region, the
00237     statistics are updated by calling <TT>stats[i].operator()(as(x))</TT>. Since
00238     the <TT>RegionStatisticsArray</TT> is passed by reference, this will overwrite
00239     the original statistics.
00240 
00241     If a candidate could be merged into more than one regions with identical
00242     cost, the algorithm will favour the nearest region. If <tt>StopAtThreshold</tt> is active, 
00243     and the cost of the current candidate at any point in the algorithm exceeds the optional 
00244     <tt>max_cost</tt> value (which defaults to <tt>NumericTraits<double>::max()</tt>), 
00245     region growing is aborted, and all voxels not yet assigned to a region remain unlabeled.
00246 
00247     In some cases, the cost only depends on the feature value of the current
00248     voxel. Then the update operation will simply be a no-op, and the <TT>cost()</TT>
00249     function returns its argument. This behavior is implemented by the
00250     \ref SeedRgDirectValueFunctor.
00251 
00252     <b> Declarations:</b>
00253 
00254     pass arguments explicitly:
00255     \code
00256     namespace vigra {
00257         template <class SrcImageIterator, class Shape, class SrcAccessor,
00258                   class SeedImageIterator, class SeedAccessor,
00259                   class DestImageIterator, class DestAccessor,
00260                   class RegionStatisticsArray, class Neighborhood>
00261         void 
00262         seededRegionGrowing3D(SrcImageIterator srcul, Shape shape, SrcAccessor as,
00263                               SeedImageIterator seedsul, SeedAccessor aseeds,
00264                               DestImageIterator destul, DestAccessor ad,
00265                               RegionStatisticsArray & stats, 
00266                               SRGType srgType = CompleteGrow,
00267                               Neighborhood neighborhood = NeighborCode3DSix(),
00268                               double max_cost = NumericTraits<double>::max());
00269     }
00270     \endcode
00271 
00272     use argument objects in conjunction with \ref ArgumentObjectFactories :
00273     \code
00274     namespace vigra {
00275         template <class SrcImageIterator, class Shape, class SrcAccessor,
00276                   class SeedImageIterator, class SeedAccessor,
00277                   class DestImageIterator, class DestAccessor,
00278                   class RegionStatisticsArray, class Neighborhood>
00279         void
00280         seededRegionGrowing3D(triple<SrcImageIterator, Shape, SrcAccessor> src,
00281                               pair<SeedImageIterator, SeedAccessor> seeds,
00282                               pair<DestImageIterator, DestAccessor> dest,
00283                               RegionStatisticsArray & stats, 
00284                               SRGType srgType = CompleteGrow,
00285                               Neighborhood neighborhood = NeighborCode3DSix(), 
00286                               double max_cost = NumericTraits<double>::max());
00287     }
00288     \endcode
00289 
00290 */
00291 doxygen_overloaded_function(template <...> void seededRegionGrowing3D)
00292 
00293 template <class SrcImageIterator, class Diff_type, class SrcAccessor,
00294           class SeedImageIterator, class SeedAccessor,
00295           class DestImageIterator, class DestAccessor,
00296           class RegionStatisticsArray, class Neighborhood>
00297 void 
00298 seededRegionGrowing3D(SrcImageIterator srcul, Diff_type shape, SrcAccessor as,
00299                       SeedImageIterator seedsul, SeedAccessor aseeds,
00300                       DestImageIterator destul, DestAccessor ad,
00301                       RegionStatisticsArray & stats, 
00302                       SRGType srgType,
00303                       Neighborhood,
00304                       double max_cost)
00305 {
00306     SrcImageIterator srclr = srcul + shape;
00307     //int w = srclr.x - srcul.x;
00308     int w = shape[0];
00309     //int h = srclr.y - srcul.y;
00310     int h = shape[1];
00311     //int d = srclr.z - srcul.z;
00312     int d = shape[2];
00313     int count = 0;
00314 
00315     SrcImageIterator isy = srcul, isx = srcul, isz = srcul;  // iterators for the src image
00316 
00317     typedef typename RegionStatisticsArray::value_type RegionStatistics;
00318     typedef typename PromoteTraits<typename RegionStatistics::cost_type, double>::Promote CostType;
00319     typedef detail::SeedRgVoxel<CostType, Diff_type> Voxel;
00320 
00321     typename Voxel::Allocator allocator;
00322 
00323     typedef std::priority_queue< Voxel *,
00324                                  std::vector<Voxel *>,
00325                                  typename Voxel::Compare >  SeedRgVoxelHeap;
00326     typedef MultiArray<3, int> IVolume;
00327 
00328     // copy seed image in an image with border
00329     Diff_type regionshape = shape + Diff_type(2,2,2);
00330     IVolume regions(regionshape);
00331     MultiIterator<3,int> ir = regions.traverser_begin();
00332     ir = ir + Diff_type(1,1,1);
00333     
00334     //IVolume::Iterator iry, irx, irz;
00335     MultiIterator<3,int> iry, irx, irz;
00336 
00337     //initImageBorder(destImageRange(regions), 1, SRGWatershedLabel);
00338     initMultiArrayBorder(destMultiArrayRange(regions), 1, SRGWatershedLabel); 
00339     
00340     copyMultiArray(seedsul, Diff_type(w,h,d), aseeds, ir, AccessorTraits<int>::default_accessor());
00341 
00342     // allocate and init memory for the results
00343 
00344     SeedRgVoxelHeap pheap;
00345     int cneighbor;
00346 
00347     #if 0
00348     static const Diff_type dist[] = { Diff_type(-1, 0, 0), Diff_type( 0,-1, 0),
00349                                       Diff_type( 1, 0, 0), Diff_type( 0, 1, 0),
00350                                       Diff_type( 0, 0,-1), Diff_type( 0, 0, 1) };
00351     #endif
00352 
00353     typedef typename Neighborhood::Direction Direction;
00354     int directionCount = Neighborhood::DirectionCount;
00355 
00356     Diff_type pos(0,0,0);
00357 
00358     for(isz=srcul, irz=ir, pos[2]=0; pos[2]<d;
00359             pos[2]++, isz.dim2()++, irz.dim2()++)
00360     {
00361         //std::cerr << "Z = " << pos[2] << std::endl;
00362 
00363         for(isy=isz, iry=irz, pos[1]=0; pos[1]<h;
00364             pos[1]++, isy.dim1()++, iry.dim1()++)
00365         {
00366             //std::cerr << "Y = " << pos[1] << std::endl;
00367             
00368             for(isx=isy, irx=iry, pos[0]=0; pos[0]<w;
00369                 pos[0]++, isx.dim0()++, irx.dim0()++)
00370             {
00371                 //std::cerr << "X = " << pos[0] << std::endl;
00372                 
00373                 if(*irx == 0)
00374                 {
00375                     // find candidate pixels for growing and fill heap
00376                     for(int i=0; i<directionCount; i++)
00377                     {
00378                         cneighbor = *(irx + Neighborhood::diff((Direction)i));
00379                         if(cneighbor > 0)
00380                         {
00381                             CostType cost = stats[cneighbor].cost(as(isx));
00382 
00383                             Voxel * voxel =
00384                                 allocator.create(pos, pos+Neighborhood::diff((Direction)i), cost, count++, cneighbor);
00385                             pheap.push(voxel);
00386                         }
00387                     }
00388                 }
00389             }
00390         }
00391     }
00392     
00393     // perform region growing
00394     while(pheap.size() != 0)
00395     {
00396         Voxel * voxel = pheap.top();
00397         pheap.pop();
00398 
00399         Diff_type pos = voxel->location_;
00400         Diff_type nearest = voxel->nearest_;
00401         int lab = voxel->label_;
00402         CostType cost = voxel->cost_;
00403 
00404         allocator.dismiss(voxel);
00405 
00406         if((srgType & StopAtThreshold) != 0 && cost > max_cost)
00407             break;
00408 
00409         irx = ir + pos;
00410         isx = srcul + pos;
00411 
00412         if(*irx) // already labelled region / watershed?
00413             continue;
00414 
00415         if((srgType & KeepContours) != 0)
00416         {
00417             for(int i=0; i<directionCount; i++)
00418             {
00419                 cneighbor = * (irx + Neighborhood::diff((Direction)i));
00420                 if((cneighbor>0) && (cneighbor != lab))
00421                 {
00422                     lab = SRGWatershedLabel;
00423                     break;
00424                 }
00425             }
00426         }
00427 
00428         *irx = lab;
00429 
00430         if((srgType & KeepContours) == 0 || lab > 0)
00431         {
00432             // update statistics
00433             stats[*irx](as(isx));
00434 
00435             // search neighborhood
00436             // second pass: find new candidate pixels
00437             for(int i=0; i<directionCount; i++)
00438             {
00439                 if(*(irx + Neighborhood::diff((Direction)i)) == 0)
00440                 {
00441                     CostType cost = stats[lab].cost(as(isx, Neighborhood::diff((Direction)i)));
00442 
00443                     Voxel * new_voxel =
00444                         allocator.create(pos+Neighborhood::diff((Direction)i), nearest, cost, count++, lab);
00445                     pheap.push(new_voxel);
00446                 }
00447             }
00448         }
00449     }
00450     
00451     // free temporary memory
00452     while(pheap.size() != 0)
00453     {
00454         allocator.dismiss(pheap.top());
00455         pheap.pop();
00456     }
00457 
00458     // write result
00459     transformMultiArray(ir, Diff_type(w,h,d), AccessorTraits<int>::default_accessor(), 
00460                         destul, ad, detail::UnlabelWatersheds());
00461 }
00462 
00463 template <class SrcImageIterator, class Diff_type, class SrcAccessor,
00464           class SeedImageIterator, class SeedAccessor,
00465           class DestImageIterator, class DestAccessor,
00466           class RegionStatisticsArray, class Neighborhood >
00467 inline void
00468 seededRegionGrowing3D(SrcImageIterator srcul, Diff_type shape, SrcAccessor as,
00469                       SeedImageIterator seedsul, SeedAccessor aseeds,
00470                       DestImageIterator destul, DestAccessor ad,
00471                       RegionStatisticsArray & stats, SRGType srgType, Neighborhood n)
00472 {
00473     seededRegionGrowing3D( srcul, shape, as, seedsul, aseeds, 
00474                            destul, ad, stats, srgType, n, NumericTraits<double>::max());
00475 }
00476 
00477 template <class SrcImageIterator, class Diff_type, class SrcAccessor,
00478           class SeedImageIterator, class SeedAccessor,
00479           class DestImageIterator, class DestAccessor,
00480           class RegionStatisticsArray >
00481 inline void
00482 seededRegionGrowing3D(SrcImageIterator srcul, Diff_type shape, SrcAccessor as,
00483                       SeedImageIterator seedsul, SeedAccessor aseeds,
00484                       DestImageIterator destul, DestAccessor ad,
00485                       RegionStatisticsArray & stats, SRGType srgType)
00486 {
00487     seededRegionGrowing3D( srcul, shape, as, seedsul, aseeds, 
00488                            destul, ad, stats, srgType, NeighborCode3DSix());
00489 }
00490 
00491 template <class SrcImageIterator, class Diff_type, class SrcAccessor,
00492           class SeedImageIterator, class SeedAccessor,
00493           class DestImageIterator, class DestAccessor,
00494           class RegionStatisticsArray >
00495 inline void
00496 seededRegionGrowing3D(SrcImageIterator srcul, Diff_type shape, SrcAccessor as,
00497                       SeedImageIterator seedsul, SeedAccessor aseeds,
00498                       DestImageIterator destul, DestAccessor ad,
00499                       RegionStatisticsArray & stats)
00500 {
00501     seededRegionGrowing3D( srcul, shape, as, seedsul, aseeds, destul, ad, 
00502                            stats, CompleteGrow);
00503 }
00504 
00505 template <class SrcImageIterator, class Shape, class SrcAccessor,
00506           class SeedImageIterator, class SeedAccessor,
00507           class DestImageIterator, class DestAccessor,
00508           class RegionStatisticsArray, class Neighborhood>
00509 inline void
00510 seededRegionGrowing3D(triple<SrcImageIterator, Shape, SrcAccessor> img1,
00511                       pair<SeedImageIterator, SeedAccessor> img3,
00512                       pair<DestImageIterator, DestAccessor> img4,
00513                       RegionStatisticsArray & stats, 
00514                       SRGType srgType, Neighborhood n, double max_cost)
00515 {
00516     seededRegionGrowing3D(img1.first, img1.second, img1.third,
00517                           img3.first, img3.second,
00518                           img4.first, img4.second,
00519                           stats, srgType, n, max_cost);
00520 }
00521 
00522 template <class SrcImageIterator, class Shape, class SrcAccessor,
00523           class SeedImageIterator, class SeedAccessor,
00524           class DestImageIterator, class DestAccessor,
00525           class RegionStatisticsArray, class Neighborhood>
00526 inline void
00527 seededRegionGrowing3D(triple<SrcImageIterator, Shape, SrcAccessor> img1,
00528                       pair<SeedImageIterator, SeedAccessor> img3,
00529                       pair<DestImageIterator, DestAccessor> img4,
00530                       RegionStatisticsArray & stats, 
00531                       SRGType srgType, Neighborhood n)
00532 {
00533     seededRegionGrowing3D(img1.first, img1.second, img1.third,
00534                           img3.first, img3.second,
00535                           img4.first, img4.second,
00536                           stats, srgType, n, NumericTraits<double>::max());
00537 }
00538 
00539 template <class SrcImageIterator, class Shape, class SrcAccessor,
00540           class SeedImageIterator, class SeedAccessor,
00541           class DestImageIterator, class DestAccessor,
00542           class RegionStatisticsArray>
00543 inline void
00544 seededRegionGrowing3D(triple<SrcImageIterator, Shape, SrcAccessor> img1,
00545                       pair<SeedImageIterator, SeedAccessor> img3,
00546                       pair<DestImageIterator, DestAccessor> img4,
00547                       RegionStatisticsArray & stats, SRGType srgType)
00548 {
00549     seededRegionGrowing3D(img1.first, img1.second, img1.third,
00550                           img3.first, img3.second,
00551                           img4.first, img4.second,
00552                           stats, srgType, NeighborCode3DSix());
00553 }
00554 
00555 template <class SrcImageIterator, class Shape, class SrcAccessor,
00556           class SeedImageIterator, class SeedAccessor,
00557           class DestImageIterator, class DestAccessor,
00558           class RegionStatisticsArray>
00559 inline void
00560 seededRegionGrowing3D(triple<SrcImageIterator, Shape, SrcAccessor> img1,
00561                       pair<SeedImageIterator, SeedAccessor> img3,
00562                       pair<DestImageIterator, DestAccessor> img4,
00563                       RegionStatisticsArray & stats)
00564 {
00565     seededRegionGrowing3D(img1.first, img1.second, img1.third,
00566                           img3.first, img3.second,
00567                           img4.first, img4.second,
00568                           stats);
00569 }
00570 
00571 } // namespace vigra
00572 
00573 #endif // VIGRA_SEEDEDREGIONGROWING_HXX
00574 

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de)
Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany

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vigra 1.7.1 (Sun Feb 19 2012)